[PDF] Top 20 HLA typing from RNA-Seq sequence reads
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HLA typing from RNA-Seq sequence reads
... NGS RNA-Seq protocol has been rapidly adopted worldwide to profile gene ...the sequence reads derived from deep sequencing the transcriptome using standard NGS RNA-Seq can ... See full document
12
Derivation of HLA types from shotgun sequence datasets
... mated HLA typing directly from NGS data ...amplifying HLA genes. The identification of allelic variants from an indi- vidual NGS data set by simple sequence search or align- ment ... See full document
8
Development of Strategies for SNP Detection in RNA Seq Data: Application to Lymphoblastoid Cell Lines and Evaluation Using 1000 Genomes Data
... duplicate reads from analysis. Duplicate reads in sequence data can occur during the PCR/library preparation steps, from sequencing artefacts such as poly-A and poly-N reads, ... See full document
9
Analysis of the Aspergillus nidulans transcriptome using high-throughput RNA sequencing
... away from agarose gels and now size select by PAGE on denaturing gels before the amplification ...removed from the official protocols, with the gel fragments instead placed directly into the PCR reaction ... See full document
264
Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data
... arising from missing signature genes and different data-normalization procedures, quanTIseq implements a full pipeline for the analysis of raw RNA-seq data that builds the mixture matrix using the ... See full document
20
Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads
... transcripts, from which we then extracted a list of putative AS ...the reads from pre-mRNAs, the largest locus that Oases predicted comprised 20,769 transcripts, while the second largest contained ... See full document
19
Multilocus Sequence Typing for Studying Genetic Relationships among Yersinia Species
... 16S RNA and MLST data did not correlate with each other, MLST was more consistent with the species’ biochemical designations than was 16S RNA ...16S RNA se- quence analysis ...16S RNA data ... See full document
11
The GATK joint genotyping workflow is appropriate for calling variants in RNA-seq experiments
... with RNA-seq data was validated using a large number of samples genotyped with alternative ...two reads and not restricting SNP calling to only highly expressed SNP (minRD ...geno- typing ... See full document
6
Aligning the Aligners: Comparison of RNA Sequencing Data Alignment and Gene Expression Quantification Tools for Clinical Breast Cancer Research
... ideal RNA-seq experiment, researchers and clinicians would acquire freshly frozen tissue samples with minimal inclusion of non-target tissues, such as blood and fat, the most common ...increased RNA ... See full document
16
SNP detection using RNA-sequences of candidate genes associated with puberty in cattle.
... bp) from Angus, Holstein, and Brangus breeds and paired-end read (100 bp) sequences from Brahman breeds were mapped to the annotated bovine reference genome ...samples from hypothalamus tissue in ... See full document
17
A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads
... to RNA-Seq (whole-transcriptome shotgun sequencing) analysis ...classify RNA sequencing data using a bioinformatics ...using RNA-Seq (whole-transcriptome shotgun sequen- cing), ... See full document
16
Limited RNA Editing in Exons of Mouse Liver and Adipose
... selected reads with base modifications of the RNA represented by at least 10 reads at the position for the edited base, located in one exon, and not corresponding to a known genomic SNP between D2 and ... See full document
27
HLAreporter: a tool for HLA typing from next generation sequencing data
... candidate HLA alleles that match those assem- bled contigs are assigned (for the scoring system and the assignment algorithm see Warren et al ...scores, HLA alleles are re- ported whenever a uniquely ... See full document
12
Human splicing diversity and the extent of unannotated splice junctions across human RNA seq samples on the Sequence Read Archive
... 20 reads across samples are accumulated by their “discovery ...database from among the samples in which the junction was ...Ranked from 1 to 5 are the dominant contributing projects from dates ... See full document
14
Genome-wide profiling of RNA editing sites in sheep
... of RNA editing sites in ...and RNA resequencing data to identify potential editing events in ...for RNA edit- ing sites only to homogenous genomic DNA (gDNA) se- quences, but heterogenous RNA ... See full document
9
Profiling tissue-resident T cell repertoires by RNA sequencing
... quences from all available RNA-seq datasets from the TCGA ...derived from 6738 solid tumor and 604 matched normal tissues, from 24 different tumor ...ranged from 0 to 702 ... See full document
8
Resolution of Ambiguous HLA Genotyping in Korean by Multi Group Specific Sequence Based Typing
... for HLA-A, -B, -C, and -DRB1 typing are summa- rized in Table 3-6, ...respectively. HLA-A*24:02:01G/*26: 01:01, *02:01:01G/*11:01:01, and *02:01:01G/*24:02:01G accounted for 6 ...the HLA-A ... See full document
9
RNA sequencing read depth requirement for optimal transcriptome coverage in Hevea brasiliensis
... Expressed Sequence Tags (ESTs) from latex ...prepared from distinct cells, tissues or organs, including RNAs from the same sample types but under different physiological conditions ...PE ... See full document
13
BAsE Seq: a method for obtaining long viral haplotypes from short sequence reads
... study RNA viruses (for example, HIV-1), or used to estimate the relative abun- dance of transcript ...long RNA templates, the future applica- tion of BAsE-Seq may be restricted to studying sub- ... See full document
14
The cnidarian Hydractinia echinata employs canonical and highly adapted histones to pack its DNA
... stage-specific RNA read mapping and transcrip- tome assemblies, RNA was extracted from adult male and female sexual polyps, adult feeding polyps and 48-h old ...removed from the samples before ... See full document
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